tbuckley/cabot-search huggingface dataset:
PATH-05. PRIMARY AND SECONDARY GLIOSARCOMA: RADIOLOGICAL AND PROGNOSTIC DIFFERENCES USING COMPREHENSIVE MULTI-OMICS ANALYSIS
Authors: Ko-Ting Chen, Ian Yi-Feng Chang, Peng-Wei Hsu, Chi-Cheng Chuang, Yin-Cheng Huang, Pin-Yuan Chen, Chen-Nen Chang, Hsuan Liu, Bertrand Chin-Ming Tan, Shih-Ming Jung, Kuo-Chen Wei
Journal: Neuro-Oncology (2023)

Abstract Purpose Gliosarcoma (GS), a rare variant of glioblastoma (GB), is further classified into primary (de novo) gliosarcoma (PGS), and secondary gliosarcoma (SGS), which is defined as recurrence after a diagnosis of diffuse glioma. Poorer survival of SGS than PGS has been reported, however, the detailed mechanism remains unknown. METHODS: A retrospective retrieval of pathological confirmed GS was performed. All the clinical, radiological, and pathological comparisons were based on the diagnosis of GS. A multi-omics, including whole exome sequencing, transcriptome, proteome and phosphoproteome, approach was used to acquire the molecular profiles of these specimens. RESULTS: From 2003 to 2020, a total of 28 GSs were identified, including 19 PGSs and 9 SGSs. The age tended to be younger in SGS group than PGS group (52.1 ± 10.9 vs. 60.8 ± 11.5, p=0.069). SGSs tended to present with dural attachment (p=0.071) and were significantly associated with major vessel encasement (p=0.002) than PGSs. The Ki-67 index tended to be higher in SGSs than PGSs (p=0.081). The GS survival was significantly shorter in SGS group than PGS group (median: 7.9 vs. 32.4 months, p&amp;lt; 0.001). The multi-omics analysis demonstrated SGSs had significantly higher expression of negative regulation of megakaryocyte differentiation, telomere capping, and DNA replication nucleosome assembly pathways than PGSs. Next, using proteome / phosphoproteome nonnegative matrix factorization analysis, PGS was categorized into two clusters (PGS_C1 versus PGS_C2) with distinct multi-omics features. Of which, PGS_C1 (n=4) tended to have shorter survival than PGS_C2 (n=15, p=0.054). Notably, the survival of patients in PGS_C1, who had similar multi-omics signature to SGS, were as poor as those of SGSs. CONCLUSIONS: In summary, this study provides, for the first time, in depth evidence for understanding GS and presents multi-omics biomarkers with prognostic significance. Further therapeutic translation should based on current findings to benefit GS patients.
PATH-06. HISTOPATHOLOGICAL CHARACTERISTICS OF TREATMENT-INDUCED EFFECTS VERSUS PROGRESSION IN 180 RE-RESECTION SAMPLES FROM IRRADIATED GLIOMAS GRADE 2-4
Authors: Christina Flies, Aline Becker, Wim van Hecke, Peter Kobalka, Pierre Robe, Tom Snijders
Journal: Neuro-Oncology (2023)

Abstract Histopathological studies of re-resected glioma tissue are considered the gold standard to distinguish actual tumor progression (TP) and treatment-induced effects (TIE) after radiotherapy. The objectives of this mono-center, retrospective cohort study were to provide detailed histopathological characterization of re-resected glioma tissue, and to correlate pathological findings with survival (data driven). Consecutive adults with a diffuse glioma (WHO grade 2-4), previously treated with (chemo-)radiation and progressive lesion were reviewed. New histological slides from the recurrent-resected tissue were prepared and stained with routine and exploratory immunohistochemical (IHC) stains. Two neuropathologists used a scoring sheet to independently assess 33 items on standard H&amp;E and IHC stains. We included 180 samples, from 165 patients. Of these, 159 samples (88.3%) originated from a second resection (first re-resection). TIE were diagnosed in 34 (19%), a mixed TIE and TP lesion in 91 (51%), and TP in 55 (31%). Median survival after first re-resection for the groups TIE, mixed and TP were respectively 14.4 (interquartile range (IQR)=8.7-42.4), 7.6 (IQR=4-12.9) and 11.5 months (IQR=7.2-25.4). A diagnosis of TIE was associated with histological findings of hyalinization, endothelial thickening, cortical infiltration, (radio)necrosis, thrombosis, lymphocytic infiltration (CD3, CD8 positive), and positivity for CD34. Percentage of viable tumor and PTBP1 stain correlated negatively with TIE. Survival in the group TIE was significantly longer than in the groups with any viable tumor (p-value of log-rank test 0.008). In multivariable Cox regression analysis, hemorrhage and higher PTBP1 positivity were associated with a poor overall survival after re-resection. Dystrophic calcifications, IDH mutations, and a higher KPS correlated with improved survival. In conclusion, we confirm the previously described characteristics of treatment-induced effects in a large consecutive cohort of re-resected diffuse gliomas. However, none of these characteristics correlated with survival. PTBP1 could be a promising marker to differentiate TIE from TP in treated glioma samples.
BIOM-43. LOSS OF NF1 PROTEIN EXPRESSION IS A POOR PROGNOSTIC BIOMARKER IN A SUBSET OF IDH-WILDTYPE GLIOBLASTOMA
Authors: Michael Chang, Viveka Chinnasamy, Maria Ioannou, Fausto Rodriguez, Calixto-Hope Lucas, Karisa Schreck
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Loss of NF1, a tumor suppressor and negative regulator of RAS signaling, is common in IDH-wildtype glioblastoma and occurs through two primary mechanisms – genomic inactivation or proteasomal degradation. NF1 loss is associated with poor clinical outcomes but may also confer sensitivity to MEK inhibitors in some tumors. No clinically validated biomarker for NF1 loss exists, limiting clinical development of therapeutics for these patients. Here, we describe an immunohistochemical biomarker for NF1 expression in IDH-wildtype glioblastoma. METHODS We constructed a tissue microarray of 73 genomically-characterized glioblastoma treated at Johns Hopkins - 45 NF1-wildtype and 28 NF1-mutant. Immunohistochemistry was performed to assess NF1 expression, then correlated with clinical and genomic characteristics. RESULTS Among NF1-mutant tumors, NF1 expression was lost in 17 specimens (77%) and retained in 5 (23%). Among NF1-wildtype tumors, NF1 expression was lost in 11 (25%), equivocal in 3 (7%), and retained in 30 (68%). Loss of NF1 expression was mutually exclusive with EGFR alterations (p = 0.034) but co-occurred with alterations in TSC2 (p = 0.02) and PIK3R1 (p = 0.049), consistent with our larger genomic patient dataset (n = 277). Loss of NF1 expression was associated with decreased median overall survival (7.3 vs 14.4 months, p = 0.027), even after correcting for prognostic variables (age, MGMT promoter methylation, extent of resection, treatment). This survival difference was driven by the subset of patients with intact genomic NF1 but loss of NF1 expression. Median overall survival in this subset (n = 11) compared to the rest of the cohort (n = 49) was 4.1 vs 13.2 months (p&amp;lt; 0.0001). Cox proportional hazards model correcting for prognostic variables revealed HR 5.4 (95%CI 1.94-15, p = 0.001) associated with loss of NF1 expression. CONCLUSION Loss of NF1 expression assessed by immunohistochemistry, particularly when paired with genomically-intact NF1, correlates with inferior outcomes in patients with glioblastoma. These results will need to be validated in a larger cohort.
SURG-28. MULTI-STAGE, OPEN CRANIAL APPROACHES FOR RESECTION OF PRIMARY INTRACRANIAL NEOPLASMS: A SYSTEMATIC REVIEW OF THE HISTORY AND CURRENT APPLICATIONS
Authors: Nicholas Bui, Nolan Brown, Cathleen Kuo, Julian Gendreau, Mickey Abraham
Journal: Neuro-Oncology (2023)

Abstract Staged surgery for skull base lesions has been utilized to facilitate maximal safe resection and optimize outcomes while minimizing morbidity and complications. Conversely, staged surgery for primary intraparenchymal neoplasms is less commonly performed and has not been reported as extensively within the literature. As such, we performed a systematic review to examine the unique surgical indications for staging, timing between stages, specific surgical approaches utilized, and postoperative complications of staged surgery for primary intra-axial neoplasms. METHODS: A literature search was conducted in August 2021 using PubMed, Web of Science, and Cochrane databases using the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) recommendations. Titles and abstracts were evaluated independently by 2 authors, after which articles were selected for final analysis based on application of strict inclusion criteria during full text screen. Each included article was then qualitatively assessed and relevant variables—including operative approaches, timing, and outcomes—were extracted for synthesis. RESULTS: Of 115 results, 7 articles were included for final analysis and consisted of 17 pediatric and 4 adult patients. Staged approaches were more commonly utilized in the pediatric patient population for resection of astrocytoma and glioma. Pediatric patients had a timing of surgeries ranging from 5–10 days between operations, compared with 18 days to 4 months in adult patients. Complications in pediatric patients were most commonly hemiparesis, hydrocephalus, cranial nerve VI and VII palsies, truncal ataxia, and cerebellar mutism, while complications in adult patients included language and abstract thinking deficits, respiratory failure, and motor weakness. CONCLUSION: This study reports the first comprehensive review of staged surgical procedures for primary, intra-axial cranial neoplasms. There exists a large degree of heterogeneity in complications resulting from staged surgeries for intra-axial neoplasms, which are similar to complications associated with single-stage surgery for intraparenchymal lesions as well as multi-stage surgeries for skull base lesions.
BIOM-05. FIRST-IN-HUMAN PROSPECTIVE TRIAL OF SONOBIOPSY IN GLIOBLASTOMA PATIENTS USING NEURONAVIGATION-GUIDED FOCUSED ULTRASOUND
Authors: Jinyun Yuan, Lu Xu, Chih-Yen Chien, Yaoheng Yang, Yimei Yue, Siaka Fadera, Andrew H Stark, Katherine Schwetye, Arash Nazeri, Rupen Desai, Umeshkumar Athiraman, Aadel Chaudhuri, Hong Chen, Eric Leuthardt
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Blood-based liquid biopsy for brain cancer offers a noninvasive alternative to invasive surgical biopsies. However, the presence of the blood-brain barrier (BBB) limits the release of brain tumor-derived molecular biomarkers into the bloodstream for sensitive diagnosis. Focused ultrasound (FUS)-enabled blood-based liquid biopsy (sonobiopsy) locally disrupts the BBB and releases tumor-derived biomarkers into blood circulation. Our previous studies have demonstrated that sonobiopsy improved the detection sensitivity of glioblastoma (GBM)-specific cirulating tumor DNA (ctDNA) in animal models of GBM. This study aimed to evaluate the feasibility and safety of sonobiopsy in enriching circulating tumor biomarkers in a first-in-human, prospective clinical trial. METHODS Five GBM patients (G01-05) were enrolled in the initial study. The sonobiopy procedures were performed prior to tumor resection, using a nimble FUS device integrated with a clinical neuronavigation system. The plasma level of glial fibrillary acidic protein (GFAP) was quantified using ultrasensitive single-molecule array (Simoa), while the cell-free DNA (cfDNA) levels were quantified using Bioanalyzer. Patient-specific tumor variants were comprehensively analyzed using a personalized tumor-informed ctDNA assay (Invitae Personalized Cancer Monitoring assay). Additionally, the two most common GBM-specific tumor variants were analyzed using customized ddPCR assays. RESULTS Analysis of plasmas collected before and after FUS sonication showed sonobiopsy enhanced plasma circulating tumor biomarker levels, including a maximum increase of 1.3-fold for GFAP, 1.6-fold for the concentration of mono-nucleosomal cfDNA fragment (120–280 bp), 1.9-fold increase in patient-specific tumor variant levels, and 5.6-fold increase in the TERT mutation level. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and nonsonicated tumor tissues found that FUS sonication mainly modulated cell physical structure-related genes. CONCLUSIONS These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
NIMG-54. CONFOCAL FLUORESCENCE ENDOMICROSCOPY: A PROSPECTIVE MULTI-CENTERED, ASSESSOR BLINDED PILOT STUDY FOR THE DIAGNOSIS OF BRAIN TUMORS
Authors: Yoon Hwan Byun, Jae-Kyung Won, Duk Hyun Hong, Ho Kang, Jang Hun Kim, Mi Ok Yu, Min-Sung Kim, Yong-Hwy Kim, Kyung-Jae Park, Min-Jae Jeong, Kyungmin Hwang, Doo-Sik Kong, Chul-Kee Park, Shin-Hyuk Kang
Journal: Neuro-Oncology (2023)

Abstract Frozen section analysis remains the gold standard for intraoperative diagnosis during brain tumor surgeries; however, it is associated with extensive time consumption and the potential for freezing artifacts. In recent years, confocal laser endomicroscopy (CLE) has been actively studied as a promising alternative to address these limitations of frozen section analysis. In this prospective, multi-centered, assessor-blinded pilot study, our aim was to evaluate the diagnostic effectiveness of cCeLL - Ex vivo, a second-generation CLE model, compared to frozen section analysis for brain tumor diagnosis. We enrolled a total of 55 patients with newly diagnosed brain tumors between October 2022 and December 2022. Biopsy samples were obtained during surgical resection, and each tissue sample was divided into three smaller samples for permanent section analysis, frozen section analysis, and imaging acquisition using cCeLL - Ex vivo. The efficacy of both frozen section analysis and cCeLL - Ex vivo was assessed by comparing their diagnoses to the results from permanent section analysis. The diagnostic accuracy of cCeLL - Ex vivo was slightly higher than that of frozen section analysis, with accuracies of 89.2% and 86.5%, respectively. Both methods demonstrated a sensitivity of 92.2%. Notably, cCeLL - Ex vivo exhibited a higher specificity of 70% compared to frozen section analysis, which had a specificity of 50%. Additionally, the mean time from sample preparation to diagnosis was significantly shorter in cCeLL - Ex vivo (13 min 17 sec) compared to frozen section analysis (28 min 28 sec). These results indicate the promising potential of cCeLL - Ex vivo as a complementary tool for intraoperative diagnosis of brain tumors. Future studies are expected to provide more evidence regarding the potential clinical utility of CLEs in clinical settings.
BIOM-38. <i>MET</i> FUSIONS AND SPLICING VARIANTS IS A STRONG ADVERSE PROGNOSTIC FACTOR IN ASTROCYTOMA, IDH-MUTANT
Authors: Kenan Zhang, Lingyu Liu, Zheng Zhao, Jing Chen, Xing Liu, Tao Jiang
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Astrocytoma, IDH-mutant is currently characterized by both histological and molecular features according to the WHO CNS5 classification. However, there were still patients with IDH-mutant lower-grade astrocytomas (LGAs, CNS WHO grade 2 and 3) who suffered poor survival. Our previous research demonstrated the enrichment and predictive role of MET fusions and/or splicing variations (MET F/SVs) in previously classified secondary IDH-mutant glioblastoma, which could be a potential complement to the existing grading system. MATERIALS We herein presented descriptive, Kaplan-Meier, multivariable Cox regression outcome analyses, and DNA methylation profiling cluster analysis in a large cohort of astrocytomas, IDH-mutant. RESULTS A total of 427 astrocytomas, IDH-mutant were included. 28/427 (6.56%) patients were defined as carrying MET F/SVs, including 9/261 (3.45%) LGAs and 19/166 (11.45%) IDH-mutant high-grade astrocytomas (HGAs, CNS WHO grade 4). The distribution of MET F/SVs was significantly different between LGAs and HGAs (p = 0.0011). Kaplan-Meier analysis of PFS and OS confirmed MET F/SVs was significantly associated with inferior survival irrespective of CNS WHO grade. Multivariable Cox regression analysis with PFS and OS as the endpoint showed MET F/SVs were independently associated with worse survival (p = 0.006 for PFS and p &amp;lt; 0.0001 for OS). Moreover, we collected 159 astrocytomas, IDH-mutant with DNA methylation profiles for further analysis. The included patients were classified into the methylation class MC astrocytoma, IDH-mutant in version 12.5 of the Heidelberg brain tumor classifier. On the t-distributed stochastic neighbor embedding (t-SNE) projection, the IDH-mutant astrocytoma with MET F/SVs was more clustered in high-grade astrocytoma (p = 0.017). CONCLUSION Collectively, we demonstrated the utmost relevance of MET F/SVs as an adverse prognostic factor in IDH-mutant astrocytoma independent of the current WHO CNS grading system. We proposed that the LGAs with MET F/SVs should be designated into CNS WHO grade 4.
EPCO-12. <i>IN VIVO</i> PERTURB-SEQ DEFINES BIOLOGICAL DRIVERS AND THERAPEUTIC VULNERABILITIES UNDERLYING RADIOTHERAPY RESISTANCE IN GLIOBLASTOMA
Authors: John Liu, Joanna Pak, Christopher Zou, Sixuan Pan, Emily Payne, Kyla Foster, Katie Lin, Tim Casey-Clyde, Kyounghee Seo, Thomas O'Loughlin, David Wu, Daniel Lim, Harish Vasudevan, Aaron Diaz, Tomoko Ozawa, Mitchel Berger, John de Groot, William Weiss, Luke Gilbert, David Raleigh
Journal: Neuro-Oncology (2023)

Abstract Glioblastomas are comprised of dynamic malignant cell states and microenvironment cell types. Mechanistic and functional studies of glioblastoma resistance to therapy have been limited by a lack of in vivo approaches for multiplexed interrogation of single cells. Here we use genome-wide and targeted CRISPR interference (CRISPRi) to identify therapeutic vulnerabilities in glioblastomas in vivo by coupling convection enhanced delivery (CED) with functional genomics and single-cell transcriptomics (perturb-seq). Human (GBM43, LN18) or mouse (GL261, SB28) glioblastomas expressing CRISPRi machinery were established intracranially in mice, and unmodified mouse glioblastomas were established intracranially in immunocompetent mice expressing CRISPRi machinery in the tumor microenvironment. Perturb-seq gene prioritization was performed using genome-wide CRISPRi screens ± radiotherapy in cell cultures. Dual-sgRNA Perturb-seq lentivirus libraries were transduced in vivo using CED, and single-cell RNA sequencing with sgRNA capture was performed ± radiotherapy. RESULTS: were validated using RNA sequencing of 254,288 single nuclei from 43 pairs of primary and recurrent patient-matched human glioblastomas. Perturb-seq ± radiotherapy of 98 genes underlying glioblastoma radiotherapy responses was performed across 414,092 single cells in vivo. Genetic perturbations reprogrammed tumor and microenvironment cell states in response to radiotherapy, and high dimensional manifolds revealed genetic dependencies in metabolic and DNA damage response pathways. The DNA-dependent protein kinase (DNA-PK) component PRKDC was identified as a driver of glioblastoma radiotherapy resistance through regulation of malignant cell-intrinsic growth and stress pathways, and regulation of malignant cell-extrinsic interferon pathways that controlled cell-cell interactions with the tumor microenvironment. PRKDC inhibition with nedisertib sensitized glioblastomas to radiotherapy and extended survival in vivo, and single-cell RNA sequencing revealed hyperactivation of cell stress and cytokine signatures with combination treatment. In summary, we report in vivo perturb-seq as a platform for simultaneous discovery and functional interrogation of therapeutic vulnerabilities in glioblastoma, and show DNA-PK inhibition sensitizes glioblastomas to radiotherapy in vivo.
MODL-34. A SERIES OF EGFR-MUTANT MODELS OF GLIOBLASTOMA THAT RECAPITULATES PATIENT TUMOR HETEROGENEITY AND RESPONSE TO TREATMENT
Authors: Katie Grausam, David Rincon Fernandez Pacheco, Emily Hatanaka, Stephen Shiao, Joshua Breunig
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is the most common and aggressive brain cancer, with a treatment regimen that has remained disappointingly unaltered for the last few decades. Preclinical testing of immunotherapy has generated promising results, sometimes leading to elimination of the tumor over time in mouse models; however, when tested clinically, patients show limited responses with no impact on patient survival. Current mouse models (e.g., GL261) for preclinical testing involve orthotopic transplantation of a cell line with tumor mutations not commonly found in patient tumors. Most of these models elicit a strong anti-tumor immune response which is typically not found clinically. Single cell sequencing has revealed that different mutations in GBM are associated with differences in the aggressiveness and composition of the tumor immune microenvironment. We therefore developed an immunocompetent, autochthonous platform for generating mouse models of GBM using combinations of clinically-relevant mutations, including mutant EGFR driving tumor growth and various single guide RNAs with CRISPR-Cas9 to elicit loss of function of tumor suppressor genes. Histopathology from tumors in mice mirrors the typical features of GBM, while single-cell RNA sequencing identified expression patterns similar to patients with different driver combinations altering expression patterns in ways that mimic their human counterparts, including the heterogeneity that is the hallmark of GBM. The immune cell population of these tumors was composed of predominantly microglia, with a small population of peripherally derived immune cells. Finally, treatment studies of radiation and anti-PD-1 using this new mouse model do not result in long-term survival, similar to human trials of these agents, paving the way for more accurate preclinical testing. In conclusion, using this unique modeling system that more closely resembles human tumors genetically and immunologically, we can better explore the mechanisms of therapeutic resistance and identify more relevant targets to improve outcomes in this challenging disease.